Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

(2022) Adrian F. Powell et al.   PLANT JOURNAL

Graph pangenome captures missing heritability and empowers tomato breeding

(2022) Yao Zhou et al.   NATURE

Brassinosteroid signaling integrates multiple pathways to release apical dominance in tomato

(2021) Xiaojian Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

(2021) Jouni Sirén et al.   SCIENCE

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

ENOregulates tomato fruit size through the floral meristem development network

(2020) Fernando J. Yuste-Lisbona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

(2020) Kaichi Huang et al.   Frontiers in Plant Science

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

De novo genome assembly of two tomato ancestors, solanum pimpinellifolium and S. lycopersicum var. cerasiforme, by long-read sequencing

(2020) Hitomi Takei et al.   DNA RESEARCH

Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters

(2019) A. P. Vasav et al.   BMC GENOMICS

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Goodbye reference, hello genome graphs

(2019) Adam Ameur   NATURE BIOTECHNOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

(2019) Aamir W. Khan et al.   TRENDS IN PLANT SCIENCE

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

(2019) Mahul Chakraborty et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

A large deletion within the clock geneLNK2contributed to the spread of tomato cultivation from Central America to Europe

(2018) Santiago Mora-García et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

A chemical genetic roadmap to improved tomato flavor

(2017) Denise Tieman et al.   SCIENCE

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Fruit weight is controlled by Cell Size Regulator encoding a novel protein that is expressed in maturing tomato fruits

(2017) Qi Mu et al.   PLoS Genetics

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

(2015) Zhonghua Zhang et al.   PLANT CELL

Jerzy Jurka – 1950–2014

(2015) Prescott Deininger   Mobile DNA

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

(2013) Tiina Särkinen et al.   BMC EVOLUTIONARY BIOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency

(2012) Rico Gamuyao et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Screening synteny blocks in pairwise genome comparisons through integer programming

(2011) Haibao Tang et al.   BMC BIOINFORMATICS

Biochemical factors contributing to tomato fruit sugar content: a review

(2011) Diane M. Beckles et al.   Fruits

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets

(2011) Miao-Xin Li et al.   HUMAN GENETICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS